This model tracks susceptibles, pre-symptomatic, asymptomatic, symptomatic, diagnosed, hopspitalized, dead and recovered hosts. The following compartments are included:
To allow more realistic distributions of movement through compartments, several of these compartments are internally split into dummy stages. Dummy stages are currently:
The included processes/mechanisms are the following:
The following interventions are implemented:
The flow diagram for the model implemented in this app is:
MIF trace plot
[1] “Alabama”
| MLE | Names |
|---|---|
| 0.4757805 | beta_s |
| 0.9998718 | max_detect_frac |
| 2.5943251 | detect_rampup |
| 22.6599060 | t_half_detect |
| 0.1400807 | frac_hosp |
| 0.5039694 | frac_dead |
| 7.6554127 | theta_cases |
| 2.5933101 | theta_hosps |
| 3.0579666 | theta_deaths |
| 0.0405373 | sigma_dw |
[1] “Alaska”
| MLE | Names |
|---|---|
| 0.2414733 | beta_s |
| 0.5689251 | max_detect_frac |
| 4.1508068 | detect_rampup |
| 20.6436619 | t_half_detect |
| 0.1258337 | frac_hosp |
| 0.2471585 | frac_dead |
| 2.4390044 | theta_cases |
| 202.8470086 | theta_hosps |
| 137.2753799 | theta_deaths |
| 0.0101502 | sigma_dw |
[1] “Arizona”
| MLE | Names |
|---|---|
| 0.4952153 | beta_s |
| 0.2979032 | max_detect_frac |
| 10.8167889 | detect_rampup |
| 15.4125146 | t_half_detect |
| 0.1297715 | frac_hosp |
| 0.7980275 | frac_dead |
| 8.3666859 | theta_cases |
| 2.6056221 | theta_hosps |
| 2.0019456 | theta_deaths |
| 0.1095120 | sigma_dw |
[1] “Arkansas”
| MLE | Names |
|---|---|
| 0.3947922 | beta_s |
| 0.7710313 | max_detect_frac |
| 1.8091734 | detect_rampup |
| 26.1276543 | t_half_detect |
| 0.0693480 | frac_hosp |
| 0.4900302 | frac_dead |
| 1.7732918 | theta_cases |
| 0.2584414 | theta_hosps |
| 853.7574251 | theta_deaths |
| 0.0131875 | sigma_dw |
[1] “California”
| MLE | Names |
|---|---|
| 0.7683454 | beta_s |
| 0.7672789 | max_detect_frac |
| 0.5753677 | detect_rampup |
| 1.1116324 | t_half_detect |
| 0.0797148 | frac_hosp |
| 0.9951985 | frac_dead |
| 2.4105247 | theta_cases |
| 44.5863558 | theta_hosps |
| 10.0492378 | theta_deaths |
| 0.3388836 | sigma_dw |
[1] “Colorado”
| MLE | Names |
|---|---|
| 0.5796489 | beta_s |
| 0.8147040 | max_detect_frac |
| 0.0625121 | detect_rampup |
| 7716.0305980 | t_half_detect |
| 0.2286327 | frac_hosp |
| 0.3959673 | frac_dead |
| 1.3471353 | theta_cases |
| 1.2006521 | theta_hosps |
| 2.6854950 | theta_deaths |
| 0.5730955 | sigma_dw |
[1] “Connecticut”
| MLE | Names |
|---|---|
| 0.6423680 | beta_s |
| 0.9999891 | max_detect_frac |
| 4.1357362 | detect_rampup |
| 12.2856042 | t_half_detect |
| 0.1842007 | frac_hosp |
| 0.9997699 | frac_dead |
| 0.6352912 | theta_cases |
| 0.0136972 | theta_hosps |
| 1.9868475 | theta_deaths |
| 0.1594647 | sigma_dw |
[1] “Delaware”
| MLE | Names |
|---|---|
| 0.4482800 | beta_s |
| 0.7082024 | max_detect_frac |
| 3.2860251 | detect_rampup |
| 27.2386718 | t_half_detect |
| 0.8159204 | frac_hosp |
| 0.0877455 | frac_dead |
| 1.2834403 | theta_cases |
| 0.0526792 | theta_hosps |
| 93.3603290 | theta_deaths |
| 0.0098450 | sigma_dw |
[1] “Florida”
| MLE | Names |
|---|---|
| 0.6373357 | beta_s |
| 0.9968498 | max_detect_frac |
| 2.1029100 | detect_rampup |
| 16.9467417 | t_half_detect |
| 0.2079825 | frac_hosp |
| 0.3865696 | frac_dead |
| 3.5265944 | theta_cases |
| 2.5916152 | theta_hosps |
| 3.4153090 | theta_deaths |
| 0.0160608 | sigma_dw |
[1] “Georgia”
| MLE | Names |
|---|---|
| 0.5678391 | beta_s |
| 0.9844980 | max_detect_frac |
| 2.9299371 | detect_rampup |
| 18.5963284 | t_half_detect |
| 0.2225743 | frac_hosp |
| 0.4927554 | frac_dead |
| 6.2849852 | theta_cases |
| 2.4615379 | theta_hosps |
| 1.2753436 | theta_deaths |
| 0.3609775 | sigma_dw |
[1] “Hawaii”
| MLE | Names |
|---|---|
| 0.3966659 | beta_s |
| 0.9083725 | max_detect_frac |
| 2.8231221 | detect_rampup |
| 35.7852040 | t_half_detect |
| 0.1665278 | frac_hosp |
| 0.1905330 | frac_dead |
| 4.2991493 | theta_cases |
| 0.9179250 | theta_hosps |
| 114.8822052 | theta_deaths |
| 0.0051709 | sigma_dw |
[1] “Idaho”
| MLE | Names |
|---|---|
| 3.8589378 | beta_s |
| 0.9944125 | max_detect_frac |
| 10.8917256 | detect_rampup |
| 31.6025373 | t_half_detect |
| 0.0562462 | frac_hosp |
| 0.9834307 | frac_dead |
| 0.3940830 | theta_cases |
| 24.3285162 | theta_hosps |
| 60.1337033 | theta_deaths |
| 0.0050602 | sigma_dw |
[1] “Illinois”
| MLE | Names |
|---|---|
| 0.6517297 | beta_s |
| 0.9980447 | max_detect_frac |
| 2.7793398 | detect_rampup |
| 19.0269305 | t_half_detect |
| 0.1057170 | frac_hosp |
| 0.9966830 | frac_dead |
| 14.9430351 | theta_cases |
| 0.0456789 | theta_hosps |
| 3.7933688 | theta_deaths |
| 0.3862127 | sigma_dw |
[1] “Indiana”
| MLE | Names |
|---|---|
| 0.4893433 | beta_s |
| 0.9988267 | max_detect_frac |
| 4.3619277 | detect_rampup |
| 20.6141564 | t_half_detect |
| 0.1559074 | frac_hosp |
| 0.9753322 | frac_dead |
| 42.7062459 | theta_cases |
| 0.0021651 | theta_hosps |
| 2.1782254 | theta_deaths |
| 0.5666347 | sigma_dw |
[1] “Iowa”
| MLE | Names |
|---|---|
| 0.5140032 | beta_s |
| 0.9819411 | max_detect_frac |
| 3.1574252 | detect_rampup |
| 27.6792387 | t_half_detect |
| 0.2631907 | frac_hosp |
| 0.2227324 | frac_dead |
| 8.5172759 | theta_cases |
| 2.5045087 | theta_hosps |
| 17.1260586 | theta_deaths |
| 0.5526685 | sigma_dw |
[1] “Kansas”
| MLE | Names |
|---|---|
| 0.4670485 | beta_s |
| 0.6249303 | max_detect_frac |
| 8.2538338 | detect_rampup |
| 13.4507017 | t_half_detect |
| 0.0928718 | frac_hosp |
| 0.2931695 | frac_dead |
| 0.7572510 | theta_cases |
| 1.3819168 | theta_hosps |
| 14.9143112 | theta_deaths |
| 0.0011814 | sigma_dw |
[1] “Kentucky”
| MLE | Names |
|---|---|
| 0.4504021 | beta_s |
| 0.5968999 | max_detect_frac |
| 17.2383267 | detect_rampup |
| 12.7250076 | t_half_detect |
| 0.3211911 | frac_hosp |
| 0.2042541 | frac_dead |
| 1.3547212 | theta_cases |
| 0.5002202 | theta_hosps |
| 8.4496537 | theta_deaths |
| 0.0075724 | sigma_dw |
[1] “Louisiana”
| MLE | Names |
|---|---|
| 0.7563637 | beta_s |
| 0.9808402 | max_detect_frac |
| 5.4206545 | detect_rampup |
| 1.6995865 | t_half_detect |
| 0.9995250 | frac_hosp |
| 0.1277534 | frac_dead |
| 3.0558676 | theta_cases |
| 1.4097063 | theta_hosps |
| 2.9749771 | theta_deaths |
| 0.6961753 | sigma_dw |
[1] “Maine”
| MLE | Names |
|---|---|
| 0.4015399 | beta_s |
| 0.2885138 | max_detect_frac |
| 3.7710738 | detect_rampup |
| 14.7487996 | t_half_detect |
| 0.1229750 | frac_hosp |
| 0.4926108 | frac_dead |
| 5.9632682 | theta_cases |
| 6148.9441984 | theta_hosps |
| 260.9166447 | theta_deaths |
| 0.0000794 | sigma_dw |
[1] “Maryland”
| MLE | Names |
|---|---|
| 0.6033276 | beta_s |
| 0.9960984 | max_detect_frac |
| 3.1837610 | detect_rampup |
| 23.3125629 | t_half_detect |
| 0.2348962 | frac_hosp |
| 0.4195236 | frac_dead |
| 6.8681600 | theta_cases |
| 6.9297887 | theta_hosps |
| 7.2241614 | theta_deaths |
| 0.0231141 | sigma_dw |
[1] “Massachusetts”
| MLE | Names |
|---|---|
| 0.7729154 | beta_s |
| 0.9154106 | max_detect_frac |
| 1.9961991 | detect_rampup |
| 0.5285161 | t_half_detect |
| 0.1939738 | frac_hosp |
| 0.9831738 | frac_dead |
| 0.7305065 | theta_cases |
| 1.0836458 | theta_hosps |
| 1.7022323 | theta_deaths |
| 0.2079888 | sigma_dw |
[1] “Michigan”
| MLE | Names |
|---|---|
| 0.6681018 | beta_s |
| 0.9993098 | max_detect_frac |
| 2.1230627 | detect_rampup |
| 0.5034660 | t_half_detect |
| 0.1630305 | frac_hosp |
| 0.7297034 | frac_dead |
| 6.2854481 | theta_cases |
| 11.8635303 | theta_hosps |
| 2.1390859 | theta_deaths |
| 0.8461073 | sigma_dw |
[1] “Minnesota”
| MLE | Names |
|---|---|
| 0.5054076 | beta_s |
| 0.6359424 | max_detect_frac |
| 1.5800931 | detect_rampup |
| 31.9776450 | t_half_detect |
| 0.2300679 | frac_hosp |
| 0.6281031 | frac_dead |
| 6.7543069 | theta_cases |
| 6.9099566 | theta_hosps |
| 13.5383492 | theta_deaths |
| 0.0000234 | sigma_dw |
[1] “Mississippi”
| MLE | Names |
|---|---|
| 2.5886407 | beta_s |
| 0.9653309 | max_detect_frac |
| 5.9199069 | detect_rampup |
| 42.8752835 | t_half_detect |
| 0.3523971 | frac_hosp |
| 0.0452218 | frac_dead |
| 0.1670806 | theta_cases |
| 0.3147402 | theta_hosps |
| 1.0696476 | theta_deaths |
| 0.0308805 | sigma_dw |
[1] “Missouri”
| MLE | Names |
|---|---|
| 0.5056369 | beta_s |
| 0.9965313 | max_detect_frac |
| 4.2806389 | detect_rampup |
| 18.4924466 | t_half_detect |
| 0.0893818 | frac_hosp |
| 0.9992059 | frac_dead |
| 2.6695570 | theta_cases |
| 1.9539823 | theta_hosps |
| 2.2036258 | theta_deaths |
| 0.0000027 | sigma_dw |
[1] “Montana”
| MLE | Names |
|---|---|
| 0.2190737 | beta_s |
| 0.9819180 | max_detect_frac |
| 5.5007664 | detect_rampup |
| 20.1344872 | t_half_detect |
| 0.1329944 | frac_hosp |
| 0.2975285 | frac_dead |
| 8.5093143 | theta_cases |
| 29.9828071 | theta_hosps |
| 9.1483486 | theta_deaths |
| 0.0624302 | sigma_dw |
[1] “Nebraska”
| MLE | Names |
|---|---|
| 0.7026193 | beta_s |
| 0.0171538 | max_detect_frac |
| 0.0541000 | detect_rampup |
| 37.0928299 | t_half_detect |
| 0.9973451 | frac_hosp |
| 0.0322449 | frac_dead |
| 3.0009511 | theta_cases |
| 0.0001652 | theta_hosps |
| 4.5408271 | theta_deaths |
| 0.0018579 | sigma_dw |
[1] “Nevada”
| MLE | Names |
|---|---|
| 0.4914973 | beta_s |
| 0.7520749 | max_detect_frac |
| 3.5079474 | detect_rampup |
| 19.9241852 | t_half_detect |
| 0.6409380 | frac_hosp |
| 0.1100404 | frac_dead |
| 6.5147477 | theta_cases |
| 967.8070642 | theta_hosps |
| 7.4327163 | theta_deaths |
| 0.0016814 | sigma_dw |
[1] “New Hampshire”
| MLE | Names |
|---|---|
| 0.4553380 | beta_s |
| 0.3978741 | max_detect_frac |
| 3.4541220 | detect_rampup |
| 20.2656428 | t_half_detect |
| 0.1238897 | frac_hosp |
| 0.6179200 | frac_dead |
| 0.6943660 | theta_cases |
| 1.4791546 | theta_hosps |
| 1.1575968 | theta_deaths |
| 0.0317890 | sigma_dw |
[1] “New Jersey”
| MLE | Names |
|---|---|
| 0.7531299 | beta_s |
| 0.9890144 | max_detect_frac |
| 2.9788748 | detect_rampup |
| 13.1645477 | t_half_detect |
| 0.1853898 | frac_hosp |
| 0.7050469 | frac_dead |
| 11.1884673 | theta_cases |
| 13.2274055 | theta_hosps |
| 2.1934997 | theta_deaths |
| 1.0887049 | sigma_dw |
[1] “New Mexico”
| MLE | Names |
|---|---|
| 4.357194e-01 | beta_s |
| 9.976292e-01 | max_detect_frac |
| 2.533738e+00 | detect_rampup |
| 4.710459e+01 | t_half_detect |
| 2.015578e-01 | frac_hosp |
| 4.145089e-01 | frac_dead |
| 3.893231e+00 | theta_cases |
| 2.050290e-01 | theta_hosps |
| 6.868251e+04 | theta_deaths |
| 4.011400e-03 | sigma_dw |
[1] “New York”
| MLE | Names |
|---|---|
| 0.8069368 | beta_s |
| 0.9631430 | max_detect_frac |
| 0.9420071 | detect_rampup |
| 1.6921558 | t_half_detect |
| 0.2205142 | frac_hosp |
| 0.3037073 | frac_dead |
| 1.1571367 | theta_cases |
| 2.5602950 | theta_hosps |
| 4.6052996 | theta_deaths |
| 1.1453825 | sigma_dw |
[1] “North Carolina”
| MLE | Names |
|---|---|
| 0.4912003 | beta_s |
| 0.7130152 | max_detect_frac |
| 3.4637861 | detect_rampup |
| 21.6184326 | t_half_detect |
| 0.9676310 | frac_hosp |
| 0.0724228 | frac_dead |
| 7.9707225 | theta_cases |
| 4773.6180369 | theta_hosps |
| 3.5601530 | theta_deaths |
| 0.0005844 | sigma_dw |
[1] “North Dakota”
| MLE | Names |
|---|---|
| 0.3604785 | beta_s |
| 0.9460589 | max_detect_frac |
| 2.3013497 | detect_rampup |
| 44.0761575 | t_half_detect |
| 0.0936381 | frac_hosp |
| 0.4513159 | frac_dead |
| 2.4972940 | theta_cases |
| 9547.0722228 | theta_hosps |
| 161.7090704 | theta_deaths |
| 0.0051387 | sigma_dw |
[1] “Ohio”
| MLE | Names |
|---|---|
| 0.4773143 | beta_s |
| 0.9485901 | max_detect_frac |
| 4.2277360 | detect_rampup |
| 17.3502993 | t_half_detect |
| 0.1827068 | frac_hosp |
| 0.4313134 | frac_dead |
| 6.9363940 | theta_cases |
| 10.2694614 | theta_hosps |
| 4.4857994 | theta_deaths |
| 0.8387246 | sigma_dw |
[1] “Oklahoma”
| MLE | Names |
|---|---|
| 0.4203167 | beta_s |
| 0.7566808 | max_detect_frac |
| 4.1509598 | detect_rampup |
| 16.8617860 | t_half_detect |
| 0.2006356 | frac_hosp |
| 0.4310370 | frac_dead |
| 4.2912841 | theta_cases |
| 0.6320082 | theta_hosps |
| 1.7204058 | theta_deaths |
| 0.0038317 | sigma_dw |
[1] “Oregon”
| MLE | Names |
|---|---|
| 0.4327268 | beta_s |
| 0.5119361 | max_detect_frac |
| 4.1487139 | detect_rampup |
| 16.7735740 | t_half_detect |
| 0.2107754 | frac_hosp |
| 0.2229556 | frac_dead |
| 1.5798511 | theta_cases |
| 1.4868724 | theta_hosps |
| 16.5543752 | theta_deaths |
| 0.0000216 | sigma_dw |
[1] “Pennsylvania”
| MLE | Names |
|---|---|
| 0.6702931 | beta_s |
| 0.9079422 | max_detect_frac |
| 2.9009401 | detect_rampup |
| 19.3592778 | t_half_detect |
| 0.1681187 | frac_hosp |
| 0.9983662 | frac_dead |
| 62.7174540 | theta_cases |
| 2.4521287 | theta_hosps |
| 0.9980466 | theta_deaths |
| 1.0248704 | sigma_dw |
[1] “Rhode Island”
| MLE | Names |
|---|---|
| 0.8198189 | beta_s |
| 0.1017122 | max_detect_frac |
| 0.8074645 | detect_rampup |
| 284.9928463 | t_half_detect |
| 0.1392710 | frac_hosp |
| 0.5527588 | frac_dead |
| 38.4599160 | theta_cases |
| 0.7603183 | theta_hosps |
| 1.7041735 | theta_deaths |
| 0.4946123 | sigma_dw |
[1] “South Carolina”
| MLE | Names |
|---|---|
| 0.4294693 | beta_s |
| 0.9901551 | max_detect_frac |
| 1.5790809 | detect_rampup |
| 28.5578336 | t_half_detect |
| 0.1998226 | frac_hosp |
| 0.4088911 | frac_dead |
| 0.3890405 | theta_cases |
| 0.0453772 | theta_hosps |
| 0.6817332 | theta_deaths |
| 0.0039764 | sigma_dw |
[1] “South Dakota”
| MLE | Names |
|---|---|
| 0.8703450 | beta_s |
| 0.0067903 | max_detect_frac |
| 8.2736680 | detect_rampup |
| 12.5196208 | t_half_detect |
| 0.0916336 | frac_hosp |
| 0.2075713 | frac_dead |
| 5.4617063 | theta_cases |
| 1885.5555854 | theta_hosps |
| 2.4653109 | theta_deaths |
| 0.8479423 | sigma_dw |
[1] “Tennessee”
| MLE | Names |
|---|---|
| 0.4725450 | beta_s |
| 0.9908922 | max_detect_frac |
| 2.1543169 | detect_rampup |
| 21.4147435 | t_half_detect |
| 0.0891754 | frac_hosp |
| 0.3192161 | frac_dead |
| 5.2637242 | theta_cases |
| 2.1406402 | theta_hosps |
| 2.1739394 | theta_deaths |
| 0.7909954 | sigma_dw |
[1] “Texas”
| MLE | Names |
|---|---|
| 0.6012227 | beta_s |
| 0.8440029 | max_detect_frac |
| 5.1786280 | detect_rampup |
| 18.6295301 | t_half_detect |
| 0.0528255 | frac_hosp |
| 0.9986054 | frac_dead |
| 4.5271595 | theta_cases |
| 353.3343351 | theta_hosps |
| 4.7091918 | theta_deaths |
| 0.2234753 | sigma_dw |
[1] “Utah”
| MLE | Names |
|---|---|
| 0.4631379 | beta_s |
| 0.9993058 | max_detect_frac |
| 2.4030697 | detect_rampup |
| 22.3376673 | t_half_detect |
| 0.0832513 | frac_hosp |
| 0.2127126 | frac_dead |
| 13.2697297 | theta_cases |
| 3726.6847360 | theta_hosps |
| 2443.8913546 | theta_deaths |
| 0.2688527 | sigma_dw |
[1] “Vermont”
| MLE | Names |
|---|---|
| 2.8242303 | beta_s |
| 0.8967214 | max_detect_frac |
| 9.6074520 | detect_rampup |
| 49.9365148 | t_half_detect |
| 0.1233905 | frac_hosp |
| 0.2797252 | frac_dead |
| 0.8904855 | theta_cases |
| 0.1178884 | theta_hosps |
| 1782.0967756 | theta_deaths |
| 0.0002420 | sigma_dw |
[1] “Virginia”
| MLE | Names |
|---|---|
| 0.5299923 | beta_s |
| 0.9242610 | max_detect_frac |
| 2.7323813 | detect_rampup |
| 28.0106273 | t_half_detect |
| 0.2304851 | frac_hosp |
| 0.3778277 | frac_dead |
| 4.2367129 | theta_cases |
| 0.8712811 | theta_hosps |
| 2.5009447 | theta_deaths |
| 0.2249052 | sigma_dw |
[1] “Washington”
| MLE | Names |
|---|---|
| 0.5110536 | beta_s |
| 0.0075791 | max_detect_frac |
| 0.2123196 | detect_rampup |
| 0.1560973 | t_half_detect |
| 0.8123395 | frac_hosp |
| 0.1284921 | frac_dead |
| 0.4268339 | theta_cases |
| 22.4491855 | theta_hosps |
| 7.2360925 | theta_deaths |
| 0.0023018 | sigma_dw |
[1] “West Virginia”
| MLE | Names |
|---|---|
| 0.3280613 | beta_s |
| 0.5807087 | max_detect_frac |
| 5.3376010 | detect_rampup |
| 23.5649314 | t_half_detect |
| 0.5489887 | frac_hosp |
| 0.1161151 | frac_dead |
| 3.2819078 | theta_cases |
| 0.0000103 | theta_hosps |
| 38.1040870 | theta_deaths |
| 0.0108008 | sigma_dw |
[1] “Wisconsin”
| MLE | Names |
|---|---|
| 0.5019510 | beta_s |
| 0.7510068 | max_detect_frac |
| 3.3567859 | detect_rampup |
| 16.5550132 | t_half_detect |
| 0.1682813 | frac_hosp |
| 0.3589507 | frac_dead |
| 6.4120375 | theta_cases |
| 5.3823749 | theta_hosps |
| 2.7594721 | theta_deaths |
| 0.0178186 | sigma_dw |
[1] “Wyoming”
| MLE | Names |
|---|---|
| 0.2944637 | beta_s |
| 0.2163054 | max_detect_frac |
| 8.5549068 | detect_rampup |
| 15.0829918 | t_half_detect |
| 0.1164160 | frac_hosp |
| 0.1397636 | frac_dead |
| 0.9861360 | theta_cases |
| 3.3417054 | theta_hosps |
| 12.1024765 | theta_deaths |
| 0.0521916 | sigma_dw |